@article{depristo11,
  title={A framework for variation discovery and genotyping using next-generation {DNA} sequencing data},
  author={DePristo, Mark A and Banks, Eric and Poplin, Ryan and Garimella, Kiran V and Maguire, Jared R and Hartl, Christopher and Philippakis, Anthony A and del Angel, Guillermo and Rivas, Manuel A and Hanna, Matt and others},
  journal={Nature Genetics},
  volume={43},
  number={5},
  pages={491--498},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{mckenna10,
  title={{The Genome Analysis Toolkit}: a {MapReduce} framework for analyzing next-generation {DNA} sequencing data},
  author={McKenna, Aaron and Hanna, Matthew and Banks, Eric and Sivachenko, Andrey and Cibulskis, Kristian and Kernytsky, Andrew and Garimella, Kiran and Altshuler, David and Gabriel, Stacey and Daly, Mark and others},
  journal={Genome Research},
  volume={20},
  number={9},
  pages={1297--1303},
  year={2010},
  publisher={Cold Spring Harbor Lab}
}

@article{picard,
  title={Picard},
  howpublished={\url{http://broadinstitute.github.io/picard/}},
  author={{The Broad Institute of Harvard and MIT}},
  year={2014}
}

@article{li10,
  title={Fast and accurate long-read alignment with {B}urrows-{W}heeler transform},
  author={Li, Heng and Durbin, Richard},
  journal={Bioinformatics},
  volume={26},
  number={5},
  pages={589--595},
  year={2010},
  publisher={Oxford Univ Press}
}

@article{nakamura11,
  title={Sequence-specific error profile of {I}llumina sequencers},
  author={Nakamura, Kensuke and Oshima, Taku and Morimoto, Takuya and Ikeda, Shun and Yoshikawa, Hirofumi and Shiwa, Yuh and Ishikawa, Shu and Linak, Margaret C and Hirai, Aki and Takahashi, Hiroki and others},
  journal={Nucleic acids research},
  pages={gkr344},
  year={2011},
  publisher={Oxford Univ Press}
}

@article{sherry01,
  title={{dbSNP}: the {NCBI} database of genetic variation},
  author={Sherry, Stephen T and Ward, M-H and Kholodov, M and Baker, J and Phan, Lon and Smigielski, Elizabeth M and Sirotkin, Karl},
  journal={Nucleic acids research},
  volume={29},
  number={1},
  pages={308--311},
  year={2001},
  publisher={Oxford Univ Press}
}

@article{smith81,
  title={Identification of common molecular subsequences},
  author={Smith, Temple F and Waterman, Michael S},
  journal={Journal of molecular biology},
  volume={147},
  number={1},
  pages={195--197},
  year={1981},
  publisher={Elsevier}
}

@article{vivian16,
  title={Rapid and efficient analysis of 20,000 {RNA}-seq samples with {Toil}},
  author={Vivian, John and Rao, Arjun and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and others},
  journal={bioRxiv},
  year={2016},
  publisher={Cold Spring Harbor Labs Journals}
}

@inproceedings{vavilapalli13,
  title={{Apache Hadoop YARN: Y}et another resource negotiator},
  author={Vavilapalli, Vinod Kumar and Murthy, Arun C and Douglas, Chris and Agarwal, Sharad and Konar, Mahadev and Evans, Robert and Graves, Thomas and Lowe, Jason and Shah, Hitesh and Seth, Siddharth and others},
  booktitle={Proceedings of the Symposium on Cloud Computing (SoCC '13)},
  pages={5},
  year={2013},
  organization={ACM}
}

@inproceedings{zaharia12,
  title={Resilient distributed datasets: {A} fault-tolerant abstraction for in-memory cluster computing},
  author={Zaharia, Matei and Chowdhury, Mosharaf and Das, Tathagata and Dave, Ankur and Ma, Justin and McCauley, Murphy and Franklin, Michael and Shenker, Scott and Stoica, Ion},
  booktitle={Proceedings of the Conference on Networked Systems Design and Implementation (NSDI '12)},
  pages={2},
  year={2012},
  organization={USENIX Association}
}

@techreport{massie13,
  title={{ADAM}: Genomics Formats and Processing Patterns for Cloud Scale Computing},
  author={Massie, Matt and Nothaft, Frank and Hartl, Christopher and Kozanitis, Christos and Schumacher, Andr{\'e} and Joseph, Anthony D and Patterson, David A},
  year={2013},
  institution={UCB/EECS-2013-207, EECS Department, University of California, Berkeley}
}

@inproceedings{nothaft15,
  title={Rethinking Data-Intensive Science Using Scalable Analytics Systems},
  author={Nothaft, Frank A and Massie, Matt and Danford, Timothy and Zhang, Zhao and Laserson, Uri and Yeksigian, Carl and Kottalam, Jey and Ahuja, Arun and Hammerbacher, Jeff and Linderman, Michael and Franklin, Michael and Joseph, Anthony D. and Patterson, David A.},
  booktitle={Proceedings of the 2015 ACM SIGMOD International Conference on Management of Data (SIGMOD '15)},
  year={2015},
  organization={ACM}
}

@inproceedings{sandberg85,
  title={Design and implementation of the Sun network filesystem},
  author={Sandberg, Russel and Goldberg, David and Kleiman, Steve and Walsh, Dan and Lyon, Bob},
  booktitle={Proceedings of The USENIX conference},
  pages={119--130},
  year={1985}
}

@article{melnik10,
  title={Dremel: interactive analysis of web-scale datasets},
  author={Melnik, Sergey and Gubarev, Andrey and Long, Jing Jing and Romer, Geoffrey and Shivakumar, Shiva and Tolton, Matt and Vassilakis, Theo},
  journal={Proceedings of the VLDB Endowment},
  volume={3},
  number={1-2},
  pages={330--339},
  year={2010},
  publisher={VLDB Endowment}
}

@inproceedings{armbrust15,
  title={Spark {SQL}: Relational Data Processing in {S}park},
  author={Armbrust, Michael and Xin, Reynold S. and Lian, Cheng and Huai, Yin and Liu, Davies and Bradley, Joseph K. and Meng, Xiangrui and Kaftan, Tomer and Franklin, Michael J. and Ghodsi, Ali and Zaharia, Matei},
  booktitle={Proceedings of the International Conference on Management of Data (SIGMOD '15)},
  year={2015}
}

@article{zimmermann80,
  title={{OSI} reference model--The {ISO} model of architecture for open systems interconnection},
  author={Zimmermann, Hubert},
  journal={IEEE Transactions on Communications},
  volume={28},
  number={4},
  pages={425--432},
  year={1980},
  publisher={IEEE}
}

@article{schadt10,
  title={Computational solutions to large-scale data management and analysis},
  author={Schadt, Eric E and Linderman, Michael D and Sorenson, Jon and Lee, Lawrence and Nolan, Garry P},
  journal={Nature reviews genetics},
  volume={11},
  number={9},
  pages={647--657},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{schatz09,
  title={{CloudBurst}: {H}ighly sensitive read mapping with {MapReduce}},
  author={Schatz, Michael C},
  journal={Bioinformatics},
  volume={25},
  number={11},
  pages={1363--1369},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{langmead09crossbow,
  title={Searching for {SNP}s with cloud computing},
  author={Langmead, Ben and Schatz, Michael C and Lin, Jimmy and Pop, Mihai and Salzberg, Steven L},
  journal={Genome biology},
  volume={10},
  number={11},
  pages={R134},
  year={2009},
  publisher={BioMed Central}
}
